Reproduction of a Three-Component (DPPC/DOPC/Cholesterol) Phase Diagram using Coarse Grained Molecular Dynamics

Pressure-temperature phase diagram for shapes of vesicles: A coarse-grained molecular dynamics study

Coarse-grained molecular dynamics simulations are performed to obtain the phase diagram for shapes of a vesicle with a variation in temperature and pressure difference across the membrane. Various interesting vesicle shapes are found, in particular, a series of shape transformations are observed for a vesicle with an initial spherical shape, which changes to a prolate shape, then an oblate shap...

Coarse Grained Molecular Dynamics

Molecular Dynamics Simulations of Freezing Behavior of Pure Water and 14% Water-NaCl Mixture Using the Coarse-Grained Model

 We performed molecular dynamics simulations using the coarse-grained model to study the freezing behavior of pure water and 14% water-salt mixture in a wide range of temperatures for a very long time around 50 nanoseconds. For the salty water, an interface in nanoscale was used. For both systems, the f...

Coarse-grained molecular dynamics simulations of biomolecules

Coarse-grained molecular dynamics (CGMD) simulations are increasingly being used to analyze the behaviors of biological systems. When appropriately used, CGMD can simulate the behaviors of molecular systems several hundred times faster than elaborate all-atom molecular dynamics simulations with similar accuracy. CGMD parameters for lipids, proteins, nucleic acids, and some artificial substances...

Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics.

Experimental and computational approaches are needed to uncover the mechanisms by which molecular motors convert chemical energy into mechanical work. In this article, we describe methods and software to generate structurally realistic models of molecular motor conformations compatible with experimental data from different sources. Coarse-grained models of molecular structures are constructed b...